The thermally induced transformation of kaolinite to metakaolin is simulated using molecular dynamics through a step-wise dehydroxylation approach. The simulation shows that the removal of structural water through dehydroxylation produces a distortion or buckling effect in the 1 : 1 Al-Si layers, which is due to the migration of the aluminium into vacant sites provided by the inter-layer spacing. The structural change is characterized by a loss of crystallinity and a concomitant change in aluminium coordination from octahedral to tetrahedral, with this study confirming the presence of 5-fold aluminium within the metakaolin structure. The degree and probability of Al migration are proportional to the amount of local disorder within the structure, which is governed by the degree of local hydroxyl group loss. This results in the formation of aluminium clusters within the layers. This study proposes that instead of a uniform structure, metakaolin exhibits regions of differing aluminium concentrations, which can have major effects in the reaction chemistry at those sites.